Author: "Céline Roques" - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Céline Roques"' showing total 36 results

Start Over Author "Céline Roques"

36 results on '"Céline Roques"'

1. The black honey bee genome: insights on specific structural elements and a first step towards pangenomes

Author: Sonia E. Eynard, Christophe Klopp, Kamila Canale-Tabet, William Marande, Céline Vandecasteele, Céline Roques, Cécile Donnadieu, Quentin Boone, Bertrand Servin, and Alain Vignal
Subjects: Animal culture, SF1-1100, Genetics, QH426-470
Abstract: Abstract Background The honey bee reference genome, HAv3.1, was produced from a commercial line sample that was thought to have a largely dominant Apis mellifera ligustica genetic background. Apis mellifera mellifera, often referred to as the black bee, has a separate evolutionary history and is the original type in western and northern Europe. Growing interest in this subspecies for conservation and non-professional apicultural practices, together with the necessity of deciphering genome backgrounds in hybrids, triggered the necessity for a specific genome assembly. Moreover, having several high-quality genomes is becoming key for taking structural variations into account in pangenome analyses. Results Pacific Bioscience technology long reads were produced from a single haploid black bee drone. Scaffolding contigs into chromosomes was done using a high-density genetic map. This allowed for re-estimation of the recombination rate, which was over-estimated in some previous studies due to mis-assemblies, which resulted in spurious inversions in the older reference genomes. The sequence continuity obtained was very high and the only limit towards continuous chromosome-wide sequences seemed to be due to tandem repeat arrays that were usually longer than 10 kb and that belonged to two main families, the 371 and 91 bp repeats, causing problems in the assembly process due to high internal sequence similarity. Our assembly was used together with the reference genome to genotype two structural variants by a pangenome graph approach with Graphtyper2. Genotypes obtained were either correct or missing, when compared to an approach based on sequencing depth analysis, and genotyping rates were 89 and 76% for the two variants. Conclusions Our new assembly for the Apis mellifera mellifera honey bee subspecies demonstrates the utility of multiple high-quality genomes for the genotyping of structural variants, with a test case on two insertions and deletions. It will therefore be an invaluable resource for future studies, for instance by including structural variants in GWAS. Having used a single haploid drone for sequencing allowed a refined analysis of very large tandem repeat arrays, raising the question of their function in the genome. High quality genome assemblies for multiple subspecies such as presented here, are crucial for emerging projects using pangenomes.
Published: 2024
Full Text: View/download PDF

2. Comparative Genome Analysis of Enterococcus cecorum Reveals Intercontinental Spread of a Lineage of Clinical Poultry Isolates

Author: Jeanne Laurentie, Valentin Loux, Christelle Hennequet-Antier, Emilie Chambellon, Julien Deschamps, Angélina Trotereau, Sylviane Furlan, Claire Darrigo, Florent Kempf, Julie Lao, Marine Milhes, Céline Roques, Benoit Quinquis, Céline Vandecasteele, Roxane Boyer, Olivier Bouchez, Francis Repoila, Jean Le Guennec, Hélène Chiapello, Romain Briandet, Emmanuelle Helloin, Catherine Schouler, Isabelle Kempf, and Pascale Serror
Subjects: Enterococcus cecorum, comparative genomics, avian pathogenesis, antimicrobial resistance, poultry, veterinary pathogens, Microbiology, QR1-502
Abstract: ABSTRACT Enterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering and mortality and requiring antimicrobial use in poultry. Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of disease-associated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last 10 years from 16 French broiler farms. Comparative genomics, genome-wide association studies, and the measured susceptibility to serum, biofilm-forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate the origin of the isolates or the phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically, and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones of E. cecorum cluster into a few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones of E. cecorum belong mainly to one phylogenetic clade. IMPORTANCE Enterococcus cecorum is an important pathogen of poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associated E. cecorum isolates. To address this need, we performed whole-genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first data set on the genetic diversity and resistome of E. cecorum strains circulating in France, we pinpoint an epidemic lineage that is probably also circulating elsewhere that should be targeted preferentially by preventive strategies in order to reduce the burden of E. cecorum-related diseases.
Published: 2023
Full Text: View/download PDF

3. The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

Author: Claude Rispe, Fabrice Legeai, Paul D. Nabity, Rosa Fernández, Arinder K. Arora, Patrice Baa-Puyoulet, Celeste R. Banfill, Leticia Bao, Miquel Barberà, Maryem Bouallègue, Anthony Bretaudeau, Jennifer A. Brisson, Federica Calevro, Pierre Capy, Olivier Catrice, Thomas Chertemps, Carole Couture, Laurent Delière, Angela E. Douglas, Keith Dufault-Thompson, Paula Escuer, Honglin Feng, Astrid Forneck, Toni Gabaldón, Roderic Guigó, Frédérique Hilliou, Silvia Hinojosa-Alvarez, Yi-min Hsiao, Sylvie Hudaverdian, Emmanuelle Jacquin-Joly, Edward B. James, Spencer Johnston, Benjamin Joubard, Gaëlle Le Goff, Gaël Le Trionnaire, Pablo Librado, Shanlin Liu, Eric Lombaert, Hsiao-ling Lu, Martine Maïbèche, Mohamed Makni, Marina Marcet-Houben, David Martínez-Torres, Camille Meslin, Nicolas Montagné, Nancy A. Moran, Daciana Papura, Nicolas Parisot, Yvan Rahbé, Mélanie Ribeiro Lopes, Aida Ripoll-Cladellas, Stéphanie Robin, Céline Roques, Pascale Roux, Julio Rozas, Alejandro Sánchez-Gracia, Jose F. Sánchez-Herrero, Didac Santesmasses, Iris Scatoni, Rémy-Félix Serre, Ming Tang, Wenhua Tian, Paul A. Umina, Manuella van Munster, Carole Vincent-Monégat, Joshua Wemmer, Alex C. C. Wilson, Ying Zhang, Chaoyang Zhao, Jing Zhao, Serena Zhao, Xin Zhou, François Delmotte, and Denis Tagu
Subjects: Arthropod genomes, Daktulosphaira vitifoliae, Gene duplications, Host plant interactions, Effectors, Biological invasions, Biology (General), QH301-705.5
Abstract: Abstract Background Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors such as pathogens and climate change. Limited understanding of the insect genetics resulted in successive outbreaks across the globe when rootstocks failed. Here we report the 294-Mb genome of D. vitifoliae as a basic tool to understand host plant manipulation, nutritional endosymbiosis, and enhance global viticulture. Results Using a combination of genome, RNA, and population resequencing, we found grape phylloxera showed high duplication rates since its common ancestor with aphids, but similarity in most metabolic genes, despite lacking obligate nutritional symbioses and feeding from parenchyma. Similarly, no enrichment occurred in development genes in relation to viviparity. However, phylloxera evolved > 2700 unique genes that resemble putative effectors and are active during feeding. Population sequencing revealed the global invasion began from the upper Mississippi River in North America, spread to Europe and from there to the rest of the world. Conclusions The grape phylloxera genome reveals genetic architecture relative to the evolution of nutritional endosymbiosis, viviparity, and herbivory. The extraordinary expansion in effector genes also suggests novel adaptations to plant feeding and how insects induce complex plant phenotypes, for instance galls. Finally, our understanding of the origin of this invasive species and its genome provide genetics resources to alleviate rootstock bottlenecks restricting the advancement of viticulture.
Published: 2020
Full Text: View/download PDF

4. Genome Sequence of the Euryhaline Javafish Medaka, Oryzias javanicus: A Small Aquarium Fish Model for Studies on Adaptation to Salinity

Author: Yusuke Takehana, Margot Zahm, Cédric Cabau, Christophe Klopp, Céline Roques, Olivier Bouchez, Cécile Donnadieu, Celia Barrachina, Laurent Journot, Mari Kawaguchi, Shigeki Yasumasu, Satoshi Ansai, Kiyoshi Naruse, Koji Inoue, Chuya Shinzato, Manfred Schartl, Yann Guiguen, and Amaury Herpin
Subjects: medaka, evolution, whole genome sequencing, long reads, genetic map, transcriptome, adaptation, salinity, Genetics, QH426-470
Abstract: The genus Oryzias consists of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behavior, morphology or adaptation through comparative genomic approaches, all medaka species share many advantages of experimental model organisms including small size and short generation time, transparent embryos and genome editing tools for reverse and forward genetic studies. The Java medaka, Oryzias javanicus, is one of the two species of medaka perfectly adapted for living in brackish/sea-waters. Being an important component of the mangrove ecosystem, O. javanicus is also used as a valuable marine test-fish for ecotoxicology studies. Here, we sequenced and assembled the whole genome of O. javanicus, and anticipate this resource will be catalytic for a wide range of comparative genomic, phylogenetic and functional studies. Complementary sequencing approaches including long-read technology and data integration with a genetic map allowed the final assembly of 908 Mbp of the O. javanicus genome. Further analyses estimate that the O. javanicus genome contains 33% of repeat sequences and has a heterozygosity of 0.96%. The achieved draft assembly contains 525 scaffolds with a total length of 809.7 Mbp, a N50 of 6,3 Mbp and a L50 of 37 scaffolds. We identified 21454 predicted transcripts for a total transcriptome size of 57, 146, 583 bps. We provide here a high-quality chromosome scale draft genome assembly of the euryhaline Javafish medaka (321 scaffolds anchored on 24 chromosomes (representing 97.7% of the total bases)), and give emphasis on the evolutionary adaptation to salinity.
Published: 2020
Full Text: View/download PDF

5. Correction to: The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

Author: Claude Rispe, Fabrice Legeai, Paul D. Nabity, Rosa Fernández, Arinder K. Arora, Patrice Baa-Puyoulet, Celeste R. Banfill, Leticia Bao, Miquel Barberà, Maryem Bouallègue, Anthony Bretaudeau, Jennifer A. Brisson, Federica Calevro, Pierre Capy, Olivier Catrice, Thomas Chertemps, Carole Couture, Laurent Delière, Angela E. Douglas, Keith Dufault-Thompson, Paula Escuer, Honglin Feng, Astrid Forneck, Toni Gabaldón, Roderic Guigó, Frédérique Hilliou, Silvia Hinojosa-Alvarez, Yi-min Hsiao, Sylvie Hudaverdian, Emmanuelle Jacquin-Joly, Edward B. James, Spencer Johnston, Benjamin Joubard, Gaëlle Le Goff, Gaël Le Trionnaire, Pablo Librado, Shanlin Liu, Eric Lombaert, Hsiao-ling Lu, Martine Maïbèche, Mohamed Makni, Marina Marcet-Houben, David Martínez-Torres, Camille Meslin, Nicolas Montagné, Nancy A. Moran, Daciana Papura, Nicolas Parisot, Yvan Rahbé, Mélanie Ribeiro Lopes, Aida Ripoll-Cladellas, Stéphanie Robin, Céline Roques, Pascale Roux, Julio Rozas, Alejandro Sánchez-Gracia, Jose F. Sánchez-Herrero, Didac Santesmasses, Iris Scatoni, Rémy-Félix Serre, Ming Tang, Wenhua Tian, Paul A. Umina, Manuella van Munster, Carole Vincent-Monégat, Joshua Wemmer, Alex C. C. Wilson, Ying Zhang, Chaoyang Zhao, Jing Zhao, Serena Zhao, Xin Zhou, François Delmotte, and Denis Tagu
Subjects: Biology (General), QH301-705.5
Abstract: An amendment to this paper has been published and can be accessed via the original article.
Published: 2020
Full Text: View/download PDF

6. Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation.

Author: Qiaowei Pan, Romain Feron, Ayaka Yano, René Guyomard, Elodie Jouanno, Estelle Vigouroux, Ming Wen, Jean-Mickaël Busnel, Julien Bobe, Jean-Paul Concordet, Hugues Parrinello, Laurent Journot, Christophe Klopp, Jérôme Lluch, Céline Roques, John Postlethwait, Manfred Schartl, Amaury Herpin, and Yann Guiguen
Subjects: Genetics, QH426-470
Abstract: Teleost fishes, thanks to their rapid evolution of sex determination mechanisms, provide remarkable opportunities to study the formation of sex chromosomes and the mechanisms driving the birth of new master sex determining (MSD) genes. However, the evolutionary interplay between the sex chromosomes and the MSD genes they harbor is rather unexplored. We characterized a male-specific duplicate of the anti-Müllerian hormone (amh) as the MSD gene in Northern Pike (Esox lucius), using genomic and expression evidence as well as by loss-of-function and gain-of-function experiments. Using RAD-Sequencing from a family panel, we identified Linkage Group (LG) 24 as the sex chromosome and positioned the sex locus in its sub-telomeric region. Furthermore, we demonstrated that this MSD originated from an ancient duplication of the autosomal amh gene, which was subsequently translocated to LG24. Using sex-specific pooled genome sequencing and a new male genome sequence assembled using Nanopore long reads, we also characterized the differentiation of the X and Y chromosomes, revealing a small male-specific insertion containing the MSD gene and a limited region with reduced recombination. Our study reveals an unexpectedly low level of differentiation between a pair of sex chromosomes harboring an old MSD gene in a wild teleost fish population, and highlights both the pivotal role of genes from the amh pathway in sex determination, as well as the importance of gene duplication as a mechanism driving the turnover of sex chromosomes in this clade.
Published: 2019
Full Text: View/download PDF

7. A Scalable Genome-Editing-Based Approach for Mapping Multiprotein Complexes in Human Cells

Author: Mathieu Dalvai, Jeremy Loehr, Karine Jacquet, Caroline C. Huard, Céline Roques, Pauline Herst, Jacques Côté, and Yannick Doyon
Subjects: Biology (General), QH301-705.5
Abstract: Conventional affinity purification followed by mass spectrometry (AP-MS) analysis is a broadly applicable method used to decipher molecular interaction networks and infer protein function. However, it is sensitive to perturbations induced by ectopically overexpressed target proteins and does not reflect multilevel physiological regulation in response to diverse stimuli. Here, we developed an interface between genome editing and proteomics to isolate native protein complexes produced from their natural genomic contexts. We used CRISPR/Cas9 and TAL effector nucleases (TALENs) to tag endogenous genes and purified several DNA repair and chromatin-modifying holoenzymes to near homogeneity. We uncovered subunits and interactions among well-characterized complexes and report the isolation of MCM8/9, highlighting the efficiency and robustness of the approach. These methods improve and simplify both small- and large-scale explorations of protein interactions as well as the study of biochemical activities and structure-function relationships.
Published: 2015
Full Text: View/download PDF

8. Endoscopic ultrasound-guided fine-needle aspiration plus KRAS and GNAS mutation in malignant intraductal papillary mucinous neoplasm of the pancreas

Author: Barbara Bournet, Alix Vignolle-Vidoni, David Grand, Céline Roques, Florence Breibach, Jérome Cros, Fabrice Muscari, Nicolas Carrère, Janick Selves, Pierre Cordelier, and Louis Buscail
Subjects: Diseases of the digestive system. Gastroenterology, RC799-869
Abstract: Background: KRAS and GNAS mutations are common in intraductal papillary mucinous neoplasia of the pancreas (IPMN). The aims of this study were to assess the role of pre-therapeutic cytopathology combined with KRAS and GNAS mutation assays within cystic fluid sampled by endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) to predict malignancy of IPMN. Patients and methods: We prospectively included 37 IPMN patients with clinical and/or imaging predictors of malignancy (men: 24; mean age: 69.5 years). Cytopathology (performed on cystic fluid and/or IPMN nodules), KRAS (Exon 2, codon 12) and GNAS (Exon 8, codon 201) mutations assays (using TaqMan® allelic discrimination) were performed on EUS-FNA material. The final diagnosis was obtained from IPMN resections (n = 18); surgical biopsies, EUS-FNA analyses, and follow-up (n = 19): 10 and 27 IPMN were benign and malignant, respectively. Results: Sensitivity, specificity, positive and negative predictive values, and accuracy of cytopathology alone to diagnose IPMN malignancy were 55 %, 100 %, 100 %, 45 %, and 66 %, respectively. When KRAS-mutation analysis was combined with cytopathology these values were 92 %, 50 %, 83 %, 71 %, and 81 %, respectively. GNAS assays did not improve the performances of cytopathology alone or those of cytopathology plus a KRAS assay. Conclusions: In patients with a likelihood of malignant IPMN at pre-therapeutic investigation, testing for KRAS mutations in cystic fluid sampling by EUS-FNA improved the results of cytopathology for the diagnosis of malignancy whereas GNAS mutation assay did not.
Published: 2016
Full Text: View/download PDF

9. Complete mitochondrial genome sequence of the freshwater diatom Asterionella formosa

Author: Adrien Villain, Mila Kojadinovic, Carine Puppo, Laura Prioretti, Pierre Hubert, Yizhi Zhang, Gérald Grégori, Alain Roulet, Céline Roques, Jean-Michel Claverie, Brigitte Gontero, and Guillaume Blanc
Subjects: diatoms, asterionella, mitogenome, pacbio, Genetics, QH426-470
Abstract: We report the complete mitochondrial genome sequence of the freshwater diatom Asterionella formosa. The large 61.9 kb circular sequence encodes 34 proteins and 25 tRNAs that are universally conserved in other sequenced diatoms. We fully resolved a unique 24 kb region containing highly conserved repeated sequence units, possibly collocating with an origin of replication.
Published: 2017
Full Text: View/download PDF

10. An ancient truncated duplication of the anti‐Müllerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family

Author: Ming Wen, Qiaowei Pan, Elodie Jouanno, Jerome Montfort, Margot Zahm, Cédric Cabau, Christophe Klopp, Carole Iampietro, Céline Roques, Olivier Bouchez, Adrien Castinel, Cécile Donnadieu, Hugues Parrinello, Charles Poncet, Elodie Belmonte, Véronique Gautier, Jean-Christophe Avarre, Remi Dugue, Rudhy Gustiano, Trần Thị Thúy Hà, Marc Campet, Kednapat Sriphairoj, Josiane Ribolli, Fernanda L. de Almeida, Thomas Desvignes, John H. Postlethwait, Christabel Floi Bucao, Marc Robinson-Rechavi, Julien Bobe, Amaury Herpin, Yann Guiguen, Hunan Normal University (HNU), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Lausanne = University of Lausanne (UNIL), Plateforme Bio-Informatique - Génotoul, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-BioInfOmics, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Research Institute of Freshwater Fisheries (CRIFI-RIFF), Research Institute for Aquaculture, Neovia Asia, Kasetsart University (KU), Universidade Federal de Santa Catarina = Federal University of Santa Catarina [Florianópolis] (UFSC), Embrapa Amazônia Ocidental, Partenaires INRAE, University of Oregon [Eugene], Swiss Institute of Bioinformatics [Lausanne] (SIB), Swiss Institute of Bioinformatics [Genève] (SIB), National Institutes of Health : R01 OD011116, National Institutes of Health: R35 GM139635, ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-16-CE12-0035,GenoFish,Evolution des génes et des génomes après duplication compléte(2016), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), MING WEN, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, QIAOWEI PAN, INRAE, LPGP, ELODIE JOUANNO, INRAE, LPGP, JEROME MONTFORT, INRAE, LPGP, MARGOT ZAHM, Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAE, CÉDRIC CABAU, SIGENAE, GenPhySE, Université de Toulouse, INRAE, CHRISTOPHE KLOPP, SIGENAE, CAROLE IAMPIETRO, INRAE, CÉLINE ROQUES, INRAE, OLIVIER BOUCHEZ, INRAE, ADRIEN CASTINEL, INRAE, CÉCILE DONNADIEU, INRAE, HUGUES PARRINELLO, Montpellier GenomiX, CHARLES PONCET, GDEC Gentyane, INRAE, Université Clermont Auvergne, ELODIE BELMONTE, GDEC Gentyane, INRAE, Université Clermont Auvergne, VÉRONIQUE GAUTIER, GDEC Gentyane, INRAE, Université Clermont Auvergne, JEAN-CHRISTOPHE AVARRE, ISEM, CNRS, IRD, Univ Montpellier, REMI DUGUE, ISEM, CNRS, IRD, Univ Montpellier, RUDHY GUSTIANO, Research Institute of Freshwater Fisheries (CRIFI-RIFF), TRÂN THI THÚY HÀ, Research Institute for Aquaculture, MARC CAMPET, Neovia Asia, KEDNAPAT SRIPHAIROJ, Faculty of Natural Resources and Agro-Industry, JOSIANE RIBOLLI, Laboratório de Biologia e Cultivo de Peixes de Água Doce, Universidade Federal de Santa Catarina, FERNANDA LOUREIRO ALMEIDA OSULLIVAN, CPAA, THOMAS DESVIGNES, Institute of Neuroscience, University of Oregon, JOHN H. POSTLETHWAIT, Institute of Neuroscience, University of Oregon, CHRISTABEL FLOI BUCAO, Department of Ecology and Evolution, University of Lausanne, MARC ROBINSON-RECHAVI, Department of Ecology and Evolution, University of Lausanne, JULIEN BOBE, INRAE, LPGP, AMAURY HERPIN, INRAE, LPGP, and YANN GUIGUEN, INRAE, LPGP.
Subjects: Male, Male genome assembly, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Receptors, Peptide, Animals, Catfishes/genetics, Phylogeny, Receptors, Peptide/genetics, Receptors, Transforming Growth Factor beta/genetics, Y Chromosome/genetics, amhr2, evolution, male genome assembly, pangasiid catfishes, sex determination, Evolution, Pangasiid catfishes, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Sex determination, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Peixe-gato, Y Chromosome, Genetics, Hormônio, Receptors, Transforming Growth Factor beta, Catfishes, Ecology, Evolution, Behavior and Systematics, Biotechnology
Abstract: The evolution of sex determination (SD) mechanisms in teleost fishes is amazingly dynamic, as reflected by the variety of different master sex-determining genes identified, even sometimes among closely related species. Pangasiids are a group of economically important catfishes in many South-Asian countries, but little is known about their sex determination system. Here, we generated novel genomic resources for 12 Pangasiid species and provided a first characterization of their SD system. Based on an Oxford Nanopore long-read chromosome-scale high quality genome assembly of the striped catfish Pangasianodon hypophthalmus, we identified a duplication of the anti-Müllerian hormone receptor type II gene (amhr2), which was further characterized as being sex-linked in males and expressed only in testicular samples. These first results point to a male-specific duplication on the Y chromosome (amhr2by) of the autosomal amhr2a. Sequence annotation revealed that the P. hypophthalmus Amhr2by is truncated in its N-terminal domain, lacking the cysteine-rich extracellular part of the receptor that is crucial for ligand binding, suggesting a potential route for its neofunctionalization. Short-read genome sequencing and reference-guided assembly of 11 additional Pangasiid species, along with sex-linkage studies, revealed that this truncated amhr2by duplication is also conserved as a male-specific gene in many Pangasiids. Reconstructions of the amhr2 phylogeny suggested that amhr2by arose from an ancient duplication / insertion event at the root of the Siluroidei radiation that is dated around 100 million years ago. Altogether these results bring multiple lines of evidence supporting that amhr2by is an ancient and conserved master sex-determining gene in Pangasiid catfishes, a finding that highlights the recurrent usage of the transforming growth factor β pathway in teleost sex determination and brings another empirical case towards the understanding of the dynamics or stability of sex determination systems.
Published: 2022
Full Text: View/download PDF

11. Generation of a chromosome‐level genome assembly for Pacific halibut ( Hippoglossus stenolepis ) and characterization of its sex‐determining genomic region

Author: Andrew J. Jasonowicz, Anna Simeon, Margot Zahm, Cédric Cabau, Christophe Klopp, Céline Roques, Carole Iampietro, Jérôme Lluch, Cécile Donnadieu, Hugues Parrinello, Daniel P. Drinan, Lorenz Hauser, Yann Guiguen, and Josep V. Planas
Subjects: Male, Fishes, Genetics, Animals, Female, Flounder, Genomics, Chromosomes, Ecosystem, Ecology, Evolution, Behavior and Systematics, Genome-Wide Association Study, Biotechnology
Abstract: The Pacific halibut (Hippoglossus stenolepis) is a key species in the North Pacific Ocean and Bering Sea ecosystems, where it also supports important fisheries. However, the lack of genomic resources limits our understanding of evolutionary, environmental and anthropogenic forces affecting key life history characteristics of Pacific halibut and prevents the application of genomic tools in fisheries management and conservation efforts. In the present study, we report on the first generation of a high-quality chromosome-level assembly of the Pacific halibut genome, with an estimated size of 602 Mb, 24 chromosome-length scaffolds that contain 99.8% of the assembly and a N
Published: 2022
Full Text: View/download PDF

12. Genome structures resolve the early diversification of teleost fishes

Author: Elise Parey, Alexandra Louis, Jerome Montfort, Olivier Bouchez, Céline Roques, Carole Iampietro, Jerome Lluch, Adrien Castinel, Cécile Donnadieu, Thomas Desvignes, Christabel Floi Bucao, Elodie Jouanno, Ming Wen, Sahar Mejri, Ron Dirks, Hans Jansen, Christiaan Henkel, Wei-Jen Chen, Margot Zahm, Cédric Cabau, Christophe Klopp, Andrew W. Thompson, Marc Robinson-Rechavi, Ingo Braasch, Guillaume Lecointre, Julien Bobe, John H. Postlethwait, Camille Berthelot, Hugues Roest Crollius, Yann Guiguen, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Oregon [Eugene], Université de Lausanne = University of Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Hunan Normal University (HNU), Florida Atlantic University [Boca Raton], Future Genomics Technologies, Universiteit Leiden, Norwegian University of Life Sciences (NMBU), National Taiwan University [Taiwan] (NTU), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Western Michigan University [Kalamazoo], Michigan State University [East Lansing], Michigan State University System, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Génomique fonctionnelle comparative - Comparative functional genomics, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), This work was supported by the Agence Nationale de la Recherche, France (ANR) on the GenoFish project, 2016–2021 (grant No. ANR-16-CE12-003) to H.R.C., C.B., J.B., J.H.P., M.R.C., and Y.G., and by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by ANR (grant No. ANR-10-INBS-09) to C.D. Part of the fellowship to E.P. was supported by funds from the European Union Horizon 2020 research and innovation program under Grant Agreement No 817923 (AQUA-FAANG). M.R.-R. was supported by the Swiss National Science Foundation grant 31003A_173048. J.H.P and I.B were supported by the National Institutes of Health under grant agreement No. R01OD011116. W.J.C. was supported by MOST grants No. 111-2611-M-002-025, 110-2611-M-002-013, and 108-2611-M-002-012-MY2., ANR-16-CE12-0035,GenoFish,Evolution des génes et des génomes après duplication compléte(2016), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), European Project: 817923,H2020,H2020-EU.3.2.1.1., H2020-EU.3.2.3.1.,AQUA-FAANG(2019), DYnamique et Organisation des GENomes - Equipe de l'IBENS (DYOGEN), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Institute of Oceanography [Taipei], Plateforme Bio-Informatique - Génotoul, Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-BioInfOmics, Génétique des génomes - Genetics of Genomes (UMR 3525), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Swiss National Science Foundation grant 31003A_173048, National Institute of Health under grant agreement No R01OD011116, and Muséum national d'Histoire naturelle (MNHN)
Subjects: Animals, Zebrafish/genetics, Fishes/genetics, Eels/genetics, Biological Evolution, Phylogeny, Genome, Evolution, Molecular, Multidisciplinary, [SDV]Life Sciences [q-bio], [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, [SDV.BID]Life Sciences [q-bio]/Biodiversity
Abstract: Accurate species phylogenies are a prerequisite for evolutionary research. Teleosts are by far the largest and the most diversified group of extant vertebrates, but relationships among the three oldest lineages of extant teleosts remain unresolved. Based on seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (bony-tongues) in a monophyletic group sister to all other teleosts, i.e., the Clupeocephala lineage. This finding resolves over 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies.One-Sentence SummaryWhole-genome analyses place Elopomorpha (tarpons, eels) and Osteoglossomorpha (bony-tongues) as sister groups at the deepest branching of crown teleosts.
Published: 2023
Full Text: View/download PDF

13. Comparative genome analysis ofEnterococcus cecorumreveals intercontinental spread of a lineage of clinical poultry isolates

Author: Jeanne Laurentie, Valentin Loux, Christelle Hennequet-Antier, Emilie Chambellon, Julien Deschamps, Angélina Trotereau, Sylviane Furlan, Claire Darrigo, Florent Kempf, Julie Lao, Marine Milhes, Céline Roques, Benoit Quinquis, Céline Vandecasteele, Roxane Boyer, Olivier Bouchez, Francis Repoila, Jean Le Guennec, Hélène Chiapello, Romain Briandet, Emmanuelle Helloin, Catherine Schouler, Isabelle Kempf, and Pascale Serror
Abstract: Enterococcus cecorumis an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering, mortality, and requiring antimicrobial use in poultry. Paradoxically,E. cecorumis a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of disease-associated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last ten years in 16 French broiler farms. Comparative genomics, genome-wide association study, and measured susceptibility to serum, biofilm forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate origin of the isolates or phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones ofE. cecorumcluster in few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones ofE. cecorumbelong mainly to one phylogenetic clade.IMPORTANCEEnterococcus cecorumis an important pathogen in poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associatedE. cecorumisolates. To address this need, we performed whole genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first dataset on the genetic diversity and resistome ofE. cecorumstrains circulating in France, we pinpoint an epidemic lineage probably also circulating elsewhere and which should be targeted preferentially by preventive strategies in order to reduce the burden ofE. cecorum-related diseases.
Published: 2022
Full Text: View/download PDF

14. Abstract PS5-16: Impact of drug-drug interaction on palbociclib serum levels: Interest of therapeutic drug monitoring

Author: Fanny Leenhardt, Bénédicte Marion, Claudia Muracciole-Bich, Stéphane Pouderoux, Alexandre Evrard, Catherine Perrin, Céline Roques, Litaty Mbatchi, Marie Alexandre, William Jacot, Céline Gongora, Matthieu Gracia, and Nelly Firmin
Subjects: Body surface area, Oncology, Cancer Research, education.field_of_study, medicine.medical_specialty, medicine.diagnostic_test, business.industry, Population, Palbociclib, Pharmacokinetics, Therapeutic drug monitoring, Internal medicine, medicine, Amlodipine, Dosing, education, business, medicine.drug, Pantoprazole
Abstract: Background: The CDK4/6 inhibitors palbociclib is prescribed in association with hormonal therapy for the management of metastatic breast cancer patients. Like most oral targeted drug, therapeutic drug monitoring may be used for personalize their dosage. Using a recently published dosing technique (LC-MS/MS), we aimed at evaluating the correlation between first-cycle palbociclib plasma exposition and co-medications in order to evaluate drug-drug interaction (DDI) impact under palbociclib treatment.Methods: This is an open-label phase 4 study conducted in female subjects with first-line metastatic breast cancer (NCT04025541) treated with a palbociclib-aromatase inhibitor association. Plasma concentration of palbociclib was assessed at 24 hours postdose (plasma trough concentration Ctrough) at day 15 of first cycle of treatment. A dedicated pharmacist consultation allowed the determination of clinical covariates of interest, such as weight, body surface area, ethnicity, food intake, co-medications use and DDI before Palbociclib initiation and retrospectively at the end of clinical trial. Patients were classified then according to their risk of DDI potentially leading to inhibition of CYP3A4 and/or P-glycoprotein and gastric pH increase by gastric acid-suppressive (GAS) agents (such as proton pump inhibitors, histamine H2-receptor blockers or alginic acid). Relevant drug known to have an inhibition of CYP3A4 and/or P-glycoprotein or pH-modification activity were checked in databases (e.g. DDI predictor®, Drugs.com®, Pubmed®). Results: To date, after Ctrough analysis of the 35 first cases, the geometric mean (± standard deviation [min-max]) of palbociclib plasma Ctrough was 79.5 ng/ml (± 26.1% [43.6 ng/mL - 133 ng/mL]) at day 15, similar to what reported in the PALOMA trials. No correlation between plasma concentration and body weight, body area or also age of the patients was found in our cohort. Regarding ethnicity, all the included patients were from Caucasian origin. 31% of patients (11/35) were identified of taking drugs that could cause DDI CYP3A4 and P-glycoprotein inhibition mediated (amlodipine n=3, simvastatin n=3, losartan n=2, fluconazole n=1, atorvastatin n=1, ivabradine n=1). These potential DDI interactions were associated with a significantly higher palbociclib concentration DDI subgroup (102 ng/mL vs 69 ng/mL) (p=0.000272) (Table 1). No CYP3A4 and/or P-glycoprotein inductor were reported in cohort. 1.4% of patients (5/35) were identified of taking GAS agents (pantoprazole n=2, ranitidine n=2, alginic acid n=1). We found a significantly reduction of palbociclib concentration (59.2 ng/mL vs 79.8 ng/mL) (p=0.048) in patients taking GAS medications (Table 1). Conclusion : These preliminary results, in real-life settings, obtained with our recently-published HPLC-MS/MS method, give important information on palbociclib monitoring and pharmacokinetic variability. DDI appear to have a significant impact on palbociclib plasma exposure, GAS agents are already know to modified palbociclib absorption. Additional studies are needed to characterize palbociclib plasma concentration variations between patients, and their clinical impact on efficacy and safety. The study is ongoing and will evaluate additional potential clinical and biological impact of DDI on neutropenia occurrence, on a larger population of patients. Table 1: Patients’ plasma palbociclib concentration (day 15 of cycle 1 of treatment).Plasma palbociclib concentrations (ng/ml), global cohort (n=35)Geometric mean (CV%) (min;max)79.5 (26.1%) (43.6;133)Plasma palbociclib concentrations (ng/ml), cohort with DDI CYP3A4 and P-gp mediated (n=11)Geometric mean (CV%)102 (24.3%)Plasma palbociclib concentrations (ng/ml), cohort without DDI CYP3A4 and P-gp mediated (n=24)Geometric mean (CV%)69 (19.8%)Plasma palbociclib concentrations (ng/ml), cohort with GAS treatment (n=5)Geometric mean (CV%)59.2 (15.9%)Plasma palbociclib concentrations (ng/ml), cohort without GAS treatment (n=30)Geometric mean (CV%)82.9 (26.1%) Citation Format: Fanny Leenhardt, Matthieu Gracia, Catherine Perrin, Claudia Muracciole-Bich, Bénédicte Marion, Celine Roques, Marie Alexandre, Nelly Firmin, Stephane Pouderoux, Litaty Mbatchi, Celine Gongora, William Jacot, Alexandre Evrard. Impact of drug-drug interaction on palbociclib serum levels: Interest of therapeutic drug monitoring [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS5-16.
Published: 2021
Full Text: View/download PDF

15. MRG proteins are shared by multiple protein complexes with distinct functions

Author: Maëva Devoucoux, Céline Roques, Catherine Lachance, Anahita Lashgari, Charles Joly-Beauparlant, Karine Jacquet, Nader Alerasool, Alexandre Prudente, Mikko Taipale, Arnaud Droit, Jean-Philippe Lambert, Samer M.I. Hussein, and Jacques Côté
Subjects: biology, Chemistry, Protein subunit, Histone acetyltransferase, Biochemistry, Chromatin, Nucleosomes, Analytical Chemistry, Cell biology, Chromodomain, Bromodomain, Histones, Histone methyltransferase, biology.protein, Humans, Nucleosome, Histone deacetylase, Molecular Biology, Histone Acetyltransferases, Transcription Factors
Abstract: MRG15/MORF4L1 is a highly conserved protein in eukaryotes that contains a chromodomain recognizing H3K36me3 in chromatin. Intriguingly, it has been reported in the literature to interact with several different factors involved in chromatin modifications, gene regulation, alternative mRNA splicing and DNA repair by homologous recombination. In order to get a complete and reliable picture of associations in physiological conditions, we used genome editing and tandem affinity purification to analyze the stable native interactome of human MRG15, its paralog MRGX/MORF4L2 that lacks the chromodomain, and MRGBP (MRG-binding protein) in isogenic K562 cells. We found stable interchangeable association of MRG15 and MRGX with the NuA4/TIP60 histone acetyltransferase/chromatin remodeler, Sin3B histone deacetylase/demethylase, ASH1L histone methyltransferase and PALB2/BRCA2 DNA repair protein complexes. These associations were further confirmed and analyzed by CRISPR-tagging of endogenous proteins and comparison of expressed isoforms. Importantly, based on structural information, point mutations could be introduced that can specifically disrupt MRG15 association with some complexes but not others. Most interestingly, we also identified a new abundant native complex formed by MRG15/X-MRGBP-BRD8-EP400NL that is functionally similar to the yeast TINTIN (Trimer Independent of NuA4 for Transcription Interactions with Nucleosomes) complex. Our results show that EP400NL, being homologous to the N-terminal region of NuA4/TIP60 subunit EP400, creates TINTIN by competing for BRD8 association. Functional genomics indicate that human TINTIN plays a role in transcription of specific genes. This is most likely linked to the H4ac-binding bromodomain of BRD8 along the H3K36me3-binding chromodomain of MRG15 on the coding region of transcribed genes. Taken together, our data provide a complete detailed picture of human MRG proteins-associated protein complexes which is essential to understand and correlate their diverse biological functions in chromatin-based nuclear processes.HighlightsMRG15 and MRGX are stably associated with several different protein complexes important for genome expression and stability.Several MRG-containing complexes are chromatin modifiers.Specific point mutations in the MRG domain differentially affect associated complexes.A major human complex homologous to the yeast TINTIN complex is identified.The protein EP400NL competes with EP400 to functionally separate TINTIN from the NuA4/TIP60 complex.TINTIN contains a bromodomain and a chromodomain to regulate transcription.
Published: 2021
Full Text: View/download PDF

16. Author response: The rise and fall of the ancient northern pike master sex-determining gene

Author: Christophe Klopp, E. A. Interesova, Songlin Chen, Laurent Journot, Amaury Herpin, René Guyomard, Wesley A. Larson, Manfred Schartl, Louis Bernatchez, Vladimir A. Trifonov, Eric Saillant, Eric Rondeau, Hugo Verreycken, Patrick W. DeHaan, Stephen S. Curran, Yann Guiguen, Hongxia Hu, Hugo Darras, Romain Feron, Qiaowei Pan, J. Andrés López, Jérôme Lluch, Gael Pj Denys, Céline Roques, Mike Tringali, Camille Eché, Roger A. Tabor, Frederick W. Goetz, Hugues Parrinello, Elodie Jouanno, Krista M. Nichols, John H. Postlethwait, Konrad Ocalewicz, Ben F. Koop, and Frank A. von Hippel
Subjects: Geography, Zoology, computer, Gene, Pike, computer.programming_language
Published: 2020
Full Text: View/download PDF

17. Correction to: The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

Author: Marina Marcet-Houben, Spencer Johnston, Roderic Guigó, Claude Rispe, François Delmotte, Yvan Rahbé, Edward B. James, Carole Couture, Keith Dufault-Thompson, Laurent Delière, Fabrice Legeai, Patrice Baa-Puyoulet, Hsiao-ling Lu, Julio Rozas, Gaël Le Trionnaire, Sylvie Hudaverdian, Rosa Fernández, Chaoyang Zhao, Olivier Catrice, Manuella van Munster, Federica Calevro, Honglin Feng, Alex C.C. Wilson, Arinder K. Arora, Anthony Bretaudeau, Martine Maïbèche, Yi Min Hsiao, Thomas Chertemps, Maryem Bouallègue, Paula Escuer, Jing Zhao, Céline Roques, Aida Ripoll-Cladellas, Pierre Capy, Alejandro Sánchez-Gracia, Wenhua Tian, Paul D. Nabity, Pablo Librado, David Martínez-Torres, Paul A Umina, Joshua Wemmer, Stéphanie Robin, Rémy Félix Serre, Frédérique Hilliou, Nancy A. Moran, Iris Scatoni, Jennifer A. Brisson, Shanlin Liu, Mélanie Ribeiro Lopes, Gaëlle Le Goff, Pascale Roux, Nicolas Montagné, Nicolas Parisot, Jose Francisco Sánchez-Herrero, Silvia Hinojosa-Alvarez, Daciana Papura, Emmanuelle Jacquin-Joly, Ming Tang, Mohamed Makni, Astrid Forneck, Eric Lombaert, Xin Zhou, Ying Zhang, Carole Vincent-Monégat, Leticia Bao, Celeste R. Banfill, Miquel Barberà, Didac Santesmasses, Angela E. Douglas, Benjamin Joubard, Camille Meslin, Denis Tagu, Toni Gabaldón, and Serena Zhao
Subjects: Physiology, Genome, Insect, Adaptation, Biological, Plant Science, General Biochemistry, Genetics and Molecular Biology, Hemiptera, Structural Biology, Animals, Vitis, Phylloxera, lcsh:QH301-705.5, Ecology, Evolution, Behavior and Systematics, Whole genome sequencing, biology, Correction, Cell Biology, Biological Sciences, biology.organism_classification, Biological Evolution, lcsh:Biology (General), Evolutionary biology, PEST analysis, Adaptation, General Agricultural and Biological Sciences, Introduced Species, Animal Distribution, Biotechnology, Developmental Biology
Abstract: Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors such as pathogens and climate change. Limited understanding of the insect genetics resulted in successive outbreaks across the globe when rootstocks failed. Here we report the 294-Mb genome of D. vitifoliae as a basic tool to understand host plant manipulation, nutritional endosymbiosis, and enhance global viticulture.Using a combination of genome, RNA, and population resequencing, we found grape phylloxera showed high duplication rates since its common ancestor with aphids, but similarity in most metabolic genes, despite lacking obligate nutritional symbioses and feeding from parenchyma. Similarly, no enrichment occurred in development genes in relation to viviparity. However, phylloxera evolved 2700 unique genes that resemble putative effectors and are active during feeding. Population sequencing revealed the global invasion began from the upper Mississippi River in North America, spread to Europe and from there to the rest of the world.The grape phylloxera genome reveals genetic architecture relative to the evolution of nutritional endosymbiosis, viviparity, and herbivory. The extraordinary expansion in effector genes also suggests novel adaptations to plant feeding and how insects induce complex plant phenotypes, for instance galls. Finally, our understanding of the origin of this invasive species and its genome provide genetics resources to alleviate rootstock bottlenecks restricting the advancement of viticulture.
Published: 2020

18. The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

Author: Ying Zhang, Pascale Roux, Alex C.C. Wilson, Celeste R. Banfill, Roderic Guigó, Ming Tang, Carole Vincent-Monégat, Denis Tagu, Claude Rispe, Yi Min Hsiao, Angela E. Douglas, Daciana Papura, Keith Dufault-Thompson, Frédérique Hilliou, Shanlin Liu, Astrid Forneck, Nicolas Montagné, Eric Lombaert, Fabrice Legeai, Julio Rozas, Gaël Le Trionnaire, Yvan Rahbé, Anthony Bretaudeau, Jing Zhao, Silvia Hinojosa-Alvarez, Maryem Bouallègue, Joshua Wemmer, Stéphanie Robin, Jose Francisco Sánchez-Herrero, Pierre Capy, Federica Calevro, Xin Zhou, David Martínez-Torres, Martine Maïbèche, Patrice Baa-Puyoulet, Marina Marcet-Houben, Gaëlle Le Goff, Aida Ripoll-Cladellas, Mélanie Ribeiro Lopes, Wenhua Tian, Hsiao-ling Lu, François Delmotte, Toni Gabaldón, Arinder K. Arora, Paul A Umina, Rémy Félix Serre, Spencer Johnston, Olivier Catrice, Céline Roques, Paul D. Nabity, Serena Zhao, Pablo Librado, Miquel Barberà, Thomas Chertemps, Emmanuelle Jacquin-Joly, Benjamin Joubard, Leticia Bao, Jennifer A. Brisson, Camille Meslin, Honglin Feng, Manuella van Munster, Paula Escuer, Edward B. James, Rosa Fernández, Chaoyang Zhao, Mohamed Makni, Sylvie Hudaverdian, Nancy A. Moran, Iris Scatoni, Nicolas Parisot, Carole Couture, Didac Santesmasses, Laurent Delière, Alejandro Sánchez-Gracia, Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Department of Botany and Plant Sciences [Riverside], University of California [Riverside] (UCR), University of California-University of California, Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Institut de Biologia Evolutiva [Barcelona] (IBE / UPF - CSIC), Universitat Pompeu Fabra [Barcelona] (UPF), Cornell University [New York], Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Miami [Coral Gables], Universidad de la República (UDELAR), Universitat de València (UV), Faculté des Sciences Mathématiques, Physiques et Naturelles de Tunis (FST), Université de Tunis El Manar (UTM), University of Rochester [USA], Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Santé et agroécologie du vignoble (UMR SAVE), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Rhode Island (URI), Université de Barcelonne, Boyce Thompson Institute [Ithaca], Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Center for Genomic Regulation (CRG-UPF), CIBER de Epidemiología y Salud Pública (CIBERESP), Institució Catalana de Recerca i Estudis Avançats (ICREA), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), National Taiwan University [Taiwan] (NTU), Chang Gung Memorial Hospital [Taipei] (CGMH), Texas A&M University [College Station], Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Beijing Genomics Institute [Shenzhen] (BGI), China Agricultural University (CAU), MingDao University (MDU), University of Texas at Austin [Austin], Trafic et signalisation membranaires chez les bactéries (MTSB), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Sciences pour l'environnement (SPE), Centre National de la Recherche Scientifique (CNRS)-Université Pascal Paoli (UPP), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Brigham & Women’s Hospital [Boston] (BWH), Harvard Medical School [Boston] (HMS), University of California, University of Melbourne, INRAE (France), Juan de la Cierva-Incorporacion Fellowship (Government of Spain) : IJCI-2015-26627, Marie Sklodowska-Curie Fellowship : 747607, US National Institute of Food and Agriculture : 12216941, University of Miami Maytag Fellowship from the Department of Biology, William H. Evoy Graduate Research Support Fund from the Department of Biology, Molecular Biosciences Graduate Research, Award from the Department of Biology, Springer Nature, European Project: 764840,IGNITE, École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), University of California [Riverside] (UC Riverside), University of California (UC)-University of California (UC), Department of Entomology [CALS], College of Agriculture and Life Sciences [Cornell University] (CALS), Cornell University [New York]-Cornell University [New York], Universidad de la República [Montevideo] (UDELAR), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universitat de Barcelona (UB), Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), Université Nice Sophia Antipolis (1965 - 2019) (UNS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Université Pascal Paoli (UPP)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of California (UC), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon, European Commission, Ministerio de Economía y Competitividad (España), National Institute of Food and Agriculture (US), Miami University, Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique)
Subjects: 0106 biological sciences, Fil·loxera, Physiology, [SDV]Life Sciences [q-bio], Introduced species, Plant Science, 01 natural sciences, Genome, Gene duplications, Structural Biology, Vitis, lcsh:QH301-705.5, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, 0303 health sciences, education.field_of_study, Host plant interactions, Endosymbiosis, biology, food and beverages, Biological Sciences, Biological Evolution, General Agricultural and Biological Sciences, Rootstock, Infection, Daktulosphaira vitifoliae, Biotechnology, Research Article, Population, 010603 evolutionary biology, General Biochemistry, Genetics and Molecular Biology, Hemiptera, 03 medical and health sciences, Genetics, Insect pests, Animals, Plagues d'insectes, Adaptation, Biological invasions, Genomes, education, Phylloxera, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Obligate, Human Genome, Viticultura, Cell Biology, 15. Life on land, biology.organism_classification, Biological, Effectors, Climate Action, lcsh:Biology (General), 13. Climate action, Evolutionary biology, Arthropod genomes, Introduced Species, Insect, Animal Distribution, Developmental Biology
Abstract: Background: Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors such as pathogens and climate change. Limited understanding of the insect genetics resulted in successive outbreaks across the globe when rootstocks failed. Here we report the 294-Mb genome of D. vitifoliae as a basic tool to understand host plant manipulation, nutritional endosymbiosis, and enhance global viticulture. Results: Using a combination of genome, RNA, and population resequencing, we found grape phylloxera showed high duplication rates since its common ancestor with aphids, but similarity in most metabolic genes, despite lacking obligate nutritional symbioses and feeding from parenchyma. Similarly, no enrichment occurred in development genes in relation to viviparity. However, phylloxera evolved > 2700 unique genes that resemble putative effectors and are active during feeding. Population sequencing revealed the global invasion began from the upper Mississippi River in North America, spread to Europe and from there to the rest of the world. Conclusions: The grape phylloxera genome reveals genetic architecture relative to the evolution of nutritional endosymbiosis, viviparity, and herbivory. The extraordinary expansion in effector genes also suggests novel adaptations to plant feeding and how insects induce complex plant phenotypes, for instance galls. Finally, our understanding of the origin of this invasive species and its genome provide genetics resources to alleviate rootstock bottlenecks restricting the advancement of viticulture., This work has been funded by INRAE (France) and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 764840 for the ITN IGNITE project. Rosa Fernandez was funded by a Juan de la Cierva-Incorporación Fellowship (Government of Spain, IJCI-2015-26627) and a Marie Skłodowska-Curie Fellowship (747607). Angela Douglas was supported by the US National Institute of Food and Agriculture Grant 12216941. Honglin Feng was supported by a University of Miami Maytag Fellowship, William H. Evoy Graduate Research Support Fund, and a Molecular Biosciences Graduate Research Award from the Department of Biology.
Published: 2020
Full Text: View/download PDF

19. The rise and fall of the ancient northern pike master sex-determining gene

Author: Mike Tringali, Hongxia Hu, Amaury Herpin, Patrick W. DeHaan, Eric Rondeau, Louis Bernatchez, Wesley A. Larson, Manfred Schartl, Elodie Jouanno, E. A. Interesova, Yann Guiguen, Eric Saillant, Stephen S. Curran, Hugo Verreycken, Gaël P.J. Denys, Roger A. Tabor, Vladimir A. Trifonov, Hugo Darras, Christophe Klopp, Hugues Parrinello, Frederick W. Goetz, John H. Postlethwait, Qiaowei Pan, Céline Roques, J. Andrés López, Camille Eché, Jérôme Lluch, Laurent Journot, Frank A. von Hippel, Krista M. Nichols, Konrad Ocalewicz, Romain Feron, René Guyomard, Song-Lin Chen, Ben F. Koop, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Ecology and Evolution [Lausanne], Université de Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Department of Biology, University of Victoria, Northwest Fisheries Science Center (NWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Alaska Pacific University, Institut de Biologie Intégrative et des Systèmes [Québec] (IBIS), Florida Marine Research Institute, Florida Fish and Wildlife Conservation Commission, School of Ocean Science and Technology [Mississippi] (SOST), University of Southern Mississippi (USM), Gulf Coast Research Laboratory, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Patrimoine naturel (PatriNat), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Office français de la biodiversité (OFB), Department of Biological Sciences [Flagstaff], Northern Arizona University [Flagstaff], Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, College of Fisheries and Ocean Sciences (CFOS), University of Alaska [Fairbanks] (UAF), Research Institute for Nature and Forest (INBO), Department of Marine Biology and Ecology, University of Gdansk, Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Beijing Fisheries Research Institute, U.S. Fish and Wildlife Service, Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Tomsk State University [Tomsk], Siberian Branch of the Russian Academy of Sciences (SB RAS), Developmental Biochemistry, Biocenter, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), Institute of Neuroscience, University of Oregon, Eugene, Oregon, University of Oregon [Eugene], This work was supported by the Agence Nationale de la Recherche, the Deutsche Forschungsgemeinschaft (ANR/DFG, PhyloSex project, 2014–2016, SCHA 408/10–1, to YG and MS), and the U.S. National Institutes of Health (R01GM085318 to JHP). The MGX and Get-Plage core sequencing facilities were supported by France Genomique National infrastructure, funded as part of the ‘Investissement d’avenir’ program managed by the Agence Nationale pour la Recherche (contract ANR-10-INBS-09)., ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Université de Lausanne = University of Lausanne (UNIL), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Toulouse III - Paul Sabatier (UT3), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), University of Victoria [Canada] (UVIC), Qingdao National Laboratory for Marine Science and Technology, University of Gdańsk (UG), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Texas State University, Agence Nationale de la Recherche, Deutsche Forschungsgemeinschaft (ANR/DFG, PhyloSex project, 2014–2016, SCHA 408/10–1, to YG and MS), U.S. National Institutes of Health (R01GM085318 to JHP), France Genomique National infrastructure, funded as part of the ‘Investissement d’avenir’ program managed by the Agence Nationale pour la Recherche (contract ANR-10-INBS-09), Julius-Maximilians-Universität Würzburg (JMU), Corvaisier, Maryse, Blanc – Accords bilatéraux 2013 - Evolution des déterminants majeurs du sexe chez les poissons. - - PhyloSex2013 - ANR-13-ISV7-0005 - Blanc – Accords bilatéraux 2013 - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, and Przeworski, Molly (ed.)
Subjects: Male, 0106 biological sciences, 0301 basic medicine, Evolution of sexual reproduction, Lineage (evolution), [SDV]Life Sciences [q-bio], sex determination, 01 natural sciences, mudminnows, Gene Duplication, Gene duplication, Biology (General), Clade, master sex determining gene, Phylogeny, северная щука, computer.programming_language, гены, определяющие пол, 0303 health sciences, education.field_of_study, Sex Chromosomes, biology, umbridae, General Neuroscience, General Medicine, [SDV] Life Sciences [q-bio], Medicine, Female, Research Article, QH301-705.5, Demographic history, Science, Population, esocidae, Y chromosome, 010603 evolutionary biology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Animals, education, Esox, pikes, 030304 developmental biology, Pike, fish, General Immunology and Microbiology, evolutionary biology, Sex Determination Processes, biology.organism_classification, esociforms, Sexual reproduction, 030104 developmental biology, Evolutionary biology, Other, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer, Sex linkage
Abstract: Sexual reproduction is a ubiquitous basic feature of life and genetic sex determination is thus widespread, at least among eukaryotes. Understanding the remarkable diversity of sex determination mechanisms, however, is limited by the paucity of empirical studies. Here, we traced back the evolution of sex determination in an entire clade of vertebrates and uncovered that the northern pike (Esox lucius) master sex-determining gene initiated from a 65 to 90 million-year-old gene duplication and remained sex-linked on undifferentiated sex chromosomes for at least 56 million years. Contrasting with its ancient origin, we identified several independent species- or population-specific transitions of sex determination mechanisms in this lineage, including an unexpected complete and recent Y-chromosome loss in some North American northern pike populations. These findings highlight the diversity of the evolutionary fates of master sex-determining genes and raise the importance of careful considerations of population demographic history in sex determination studies. Our study also puts forward the hypothesis that occasional sex reversals and genetic bottlenecks provide a non-adaptive explanation for sex determination transitions.
Published: 2020
Full Text: View/download PDF

20. Liquid chromatography-electrospray ionization-tandem mass spectrometry method for quantitative estimation of new imiqualine leads with potent anticancer activities in rat and mouse plasma. Application to a pharmacokinetic study in mice

Author: Céline Roques, Pierre Cuq, Françoise M.M. Bressolle-Gomeni, Pierre-Antoine Bonnet, Bénédicte Marion, Adrien Chouchou, Christine Enjalbal, and Carine Deleuze-Masquéfa
Subjects: Male, 0301 basic medicine, Spectrometry, Mass, Electrospray Ionization, Bioanalysis, Electrospray ionization, Liquid-Liquid Extraction, Clinical Biochemistry, Pharmaceutical Science, Antineoplastic Agents, Mass spectrometry, High-performance liquid chromatography, Analytical Chemistry, Rats, Sprague-Dawley, Mice, Plasma, 03 medical and health sciences, 0302 clinical medicine, Pharmacokinetics, Tandem Mass Spectrometry, Cell Line, Tumor, Quinoxalines, Drug Discovery, Animals, Humans, Chromatography, High Pressure Liquid, Spectroscopy, Active metabolite, Chromatography, Chemistry, Selected reaction monitoring, Rats, Mice, Inbred C57BL, Standard curve, 030104 developmental biology, 030220 oncology & carcinogenesis
Abstract: Imidazoquinoxaline derivatives (imiqualines) are a new series of anticancer compounds. Two lead compounds (EAPB0203 and EAPB0503) with remarkable in vitro and in vivo activity on melanoma and T-cell lymphomas have been previously identified. The modulation of the chemical structure of the most active compound, EAPB0503, has led to the synthesis of two compounds, EAPB02302 and EAPB02303, 7 and 40 times more active than EAPB0503 against A375 human melanoma cancer cell line, respectively. The aim of this study was to develop and validate a sensitive and accurate liquid chromatography-electrospray ionization-tandem mass spectrometry method to simultaneously quantify EAPB02303 and its potential active metabolite, EAPB02302, in rat and mouse plasma. Analytes were detected in multiple reaction monitoring acquisition mode using an electrospray ionization detector in positive ion mode. Following a liquid-liquid extraction with ethyl acetate, analytes and internal standard were separated by HPLC reversed-phase on a C18 RP18 Nucleoshell column (2.7μm, 4.6×100mm). The method was validated according to FDA and EMA Bioanalytical Method Validation guidelines. The robustness of the method was assessed by introducing small variations in nine nominal analytical parameters. Statistical interpretation was performed by mean of the Student's t-test. Standard curves were generated via unweighted quadratic regression of calibrators (EAPB02303: 1.95-1000ng/mL, EAPB02302: 7.81-1000ng/mL in rat plasma; EAPB02303: 0.98-1000ng/mL, EAPB02302: 1.95-1000ng/mL in mouse plasma). From the analysis of QC samples, intra- and inter-assay precision and accuracy studies demonstrated %R.S.Ds.12.5% and percent deviation from nominal concentration7%. Matrix effects (mean matrix factors from 91.8-108.5% in rat plasma; and from 90.4-102.4% in mouse plasma) and stability assays (recoveries87%) were acceptable and in accordance with the guidelines. No quantifiable carryover effect was observed. The LLOQs were 1.95ng/mL for EAPB02303 and 7.81ng/mL for EAPB02302 in rat plasma, and 0.98ng/mL and 1.95ng/mL for the two compounds in mouse plasma, respectively. This method was successfully implemented to support a mouse pharmacokinetic study following a single intraperitoneal administration of EAPB02303 in male C57Bl/6 mice. The obtained pharmacokinetic parameters of EAPB02303 would be useful to optimize the dosing and the rhythm of administration for subsequent preclinical in vivo activity studies.
Published: 2018
Full Text: View/download PDF

21. Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation

Author: Amaury Herpin, Ming Wen, Jean-Paul Concordet, Julien Bobe, Jean-Mickael Busnel, René Guyomard, Estelle Vigouroux, Ayaka Yano, Jérôme Lluch, Laurent Journot, Elodie Jouanno, Romain Feron, Manfred Schartl, Yann Guiguen, Christophe Klopp, Qiaowei Pan, Hugues Parrinello, John H. Postlethwait, Céline Roques, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Department of Ecology and Evolution [Lausanne], Université de Lausanne (UNIL), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Fédération d'Ille-et-Vilaine pour la pêche et la protection du milieu aquatique [Rennes] (FDPPMA 35), Structure et Instabilité des Génomes (STRING), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Plateforme Bio-Informatique - Génotoul, Institut National de la Recherche Agronomique (INRA), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Neuroscience [Eugene, OR, États-Unis], University of Oregon [Eugene], Department of Physiological Chemistry [Würzburg, Allemagne], University of Würzburg-Biocenter [Würzburg, Allemagne], Comprehensive Cancer Center Mainfranken [Würzburg, Allemagne], University Hospital of Würzburg, Department of Biology [College Station, TX, États-Unis], Hagler Institute for Advanced Study [College Station, TX, États-Unis], Texas A&M University [College Station]-Texas A&M University [College Station], This project was supported by funds from the 'Agence Nationale de la Recherche' and the 'Deutsche Forschungsgemeinschaft' (ANR/DFG, PhyloSex project, 2014-2016) to YG and MS. The GeT core facility (JL, CR), Toulouse, France and the MGX facility, Montpellier, France (LJ, HP) were supported by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09)., ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Department of Ecology and Evolution, Sorbonne Université (SU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Institute of Neuroscience, Physiological Chemistry, Biocenter, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Hagler Institute for Advanced Study and Department of Biology, Texas A&M University System, This project was supported by funds from the 'Agence Nationale de la Recherche' and the 'Deutsche Forschungsgemeinschaft' (ANR/ DFG, PhyloSex project, 2014-2016) to YG and MS. The GeT core facility (JL, CR), Toulouse, France and the MGX facility, Montpellier, France (LJ, HP) were supported by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09), Bodescot, Myriam, Blanc – Accords bilatéraux 2013 - Evolution des déterminants majeurs du sexe chez les poissons. - - PhyloSex2013 - ANR-13-ISV7-0005 - Blanc – Accords bilatéraux 2013 - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Université de Lausanne = University of Lausanne (UNIL), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Dpt of Ecology and Evolution [Lausanne], Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), BioCampus Montpellier (BCM), Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Plateforme Bioinformatique Genotoul [Castanet-Tolosan], Institut National de la Recherche Agronomique (INRA)-Institut National de la Recherche Agronomique (INRA), GeT PlaGe, Genotoul, ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Julius-Maximilians-Universität Würzburg (JMU), and ProdInra, Migration
Subjects: Anti-Mullerian Hormone, Male, Evolution of sexual reproduction, [SDV]Life Sciences [q-bio], gène déterminant majeur du sexe, [MATH] Mathematics [math], [SDV.GEN] Life Sciences [q-bio]/Genetics, QH426-470, Animals, Genetically Modified, mâle, Database and Informatics Methods, 0302 clinical medicine, duplication de gènes, poisson, Gene Duplication, Gene duplication, Morphogenesis, Medicine and Health Sciences, chromosome sexuel, [MATH]Mathematics [math], Phylogeny, Genetics, détermination du sexe, 0303 health sciences, education.field_of_study, Sex Chromosomes, Sexual Differentiation, Chromosome Biology, Chromosome Mapping, Animals, Anti-Mullerian Hormone/genetics, Esocidae/physiology, Female, Gene Knockdown Techniques, Sex Chromosomes/genetics, Sex Determination Processes/genetics, Synteny, Genomics, [SDV] Life Sciences [q-bio], séquençage du génome, hormone antimullérienne, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Anatomy, Sequence Analysis, Genital Anatomy, différenciation sexuelle, expression des gènes, Research Article, Bioinformatics, Population, Locus (genetics), [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, [INFO] Computer Science [cs], Biology, Research and Analysis Methods, DNA sequencing, Chromosomes, reproduction, 03 medical and health sciences, esox lucius, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [INFO]Computer Science [cs], education, Molecular Biology Techniques, Gonads, Gene, Molecular Biology, 030304 developmental biology, Whole genome sequencing, [SDV.GEN]Life Sciences [q-bio]/Genetics, Sequence Assembly Tools, génome, Gene Mapping, Reproductive System, Chromosome, Biology and Life Sciences, Computational Biology, Cell Biology, Sex Determination, Sex Determination Processes, Genome Analysis, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Genetic Loci, Esocidae, Sequence Alignment, 030217 neurology & neurosurgery, Developmental Biology
Abstract: Teleost fishes, thanks to their rapid evolution of sex determination mechanisms, provide remarkable opportunities to study the formation of sex chromosomes and the mechanisms driving the birth of new master sex determining (MSD) genes. However, the evolutionary interplay between the sex chromosomes and the MSD genes they harbor is rather unexplored. We characterized a male-specific duplicate of the anti-Müllerian hormone (amh) as the MSD gene in Northern Pike (Esox lucius), using genomic and expression evidence as well as by loss-of-function and gain-of-function experiments. Using RAD-Sequencing from a family panel, we identified Linkage Group (LG) 24 as the sex chromosome and positioned the sex locus in its sub-telomeric region. Furthermore, we demonstrated that this MSD originated from an ancient duplication of the autosomal amh gene, which was subsequently translocated to LG24. Using sex-specific pooled genome sequencing and a new male genome sequence assembled using Nanopore long reads, we also characterized the differentiation of the X and Y chromosomes, revealing a small male-specific insertion containing the MSD gene and a limited region with reduced recombination. Our study reveals an unexpectedly low level of differentiation between a pair of sex chromosomes harboring an old MSD gene in a wild teleost fish population, and highlights both the pivotal role of genes from the amh pathway in sex determination, as well as the importance of gene duplication as a mechanism driving the turnover of sex chromosomes in this clade., Author summary In stark contrast to mammals and birds, a high proportion of teleosts have homomorphic sex chromosomes and display a high diversity of sex determining genes. Yet, population level knowledge of both the sex chromosome and the master sex determining gene is only available for the Japanese medaka, a model species. Here we identified and provided functional proofs of an old duplicate of anti-Müllerian hormone (Amh), a member of the Tgf- β family, as the male master sex determining gene in the Northern pike, Esox lucius. We found that this duplicate, named amhby (Y-chromosome-specific anti-Müllerian hormone paralog b), was translocated to the sub-telomeric region of the new sex chromosome, and now amhby shows strong sequence divergence as well as substantial expression pattern differences from its autosomal paralog, amha. We assembled a male genome sequence using Nanopore long reads and identified a restricted region of differentiation within the sex chromosome pair in a wild population. Our results provide insight on the conserved players in sex determination pathways, the mechanisms of sex chromosome turnover, and the diversity of levels of differentiation between homomorphic sex chromosomes in teleosts.
Published: 2019
Full Text: View/download PDF

22. Shear-dependency of the predicted ideal hematocrit

Author: Céline Roques, Jean-Frédéric Brun, Jacques Mercier, Thibault Fidani, Emmanuelle Varlet-Marie, Bénédicte Marion, Laurent Vachoud, Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Démarche intégrée pour l'obtention d'aliments de qualité (UMR Qualisud), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de La Réunion (UR)-Université de Montpellier (UM)-Avignon Université (AU)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Montpellier 1 (UM1), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), and Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Physics, hematocrit/viscosity ratio, medicine.diagnostic_test, Physiology, hematocrit, [SDV]Life Sciences [q-bio], Blood viscosity, Viscometer, Thermodynamics, Hematology, 030204 cardiovascular system & hematology, Hematocrit, 030218 nuclear medicine & medical imaging, Shear rate, 03 medical and health sciences, 0302 clinical medicine, Shear (geology), oxygen delivery index, Physiology (medical), Hemorheology, medicine, Humans, Cardiology and Cardiovascular Medicine, ComputingMilieux_MISCELLANEOUS
Abstract: The ideal hematocrit is the hematocrit (Hct) value resulting in the highest value of Hct/viscosity (h/η) ratio and can thus be predicted from viscometric measurements with the use of equations such as Quemada's one which yield the determination of the bell-shaped curve of h/η as a function of Hct. In a series of recent papers we applied this approach to various populations, using viscometry at high shear rate (1000 s-1). However the shape of this curve has been reported to be dependent on the shear rate, resulting in a right-shift in this top value when Hct increase. We present here in 11 young recreative athletes the evolution of the predicted top of the h/η curve and optimal theoretical Hct and the discrepancy between theoretical and optimal values over the range of shear rates 1 to 6000 s-1. Results show that the predicted optimal value of both h/η and Hct increases when shear rate increases and that the discrepancy between predicted laquooptimalraquo and actual values decreases and becomes almost asymptotic at very high shear (500 s-1). It is minimal at 2720 s-1. The correlation between predicted laquooptimalraquo and actual values of both parameters describes the same evolution. Therefore, it is better for assessing h/η and its agreement with theoretical values, and for determining the theoretical ideal hematocrit, to measure blood viscosity at shear rates equal or superior to 500 s-1.
Published: 2019
Full Text: View/download PDF

23. Leg electrical resistance predicts venous blood viscosity and hematocrit

Author: Constance Chevalier, Céline Roques, Laurent Vachoud, Jean-Frédéric Brun, Jacques Mercier, Emmanuelle Varlet-Marie, Thibault Fidani, Bénédicte Marion, Eric Raynaud de Mauverger, Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Démarche intégrée pour l'obtention d'aliments de qualité (UMR Qualisud), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Université de La Réunion (UR)-Université de Montpellier (UM)-Avignon Université (AU)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Montpellier 1 (UM1), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de La Réunion (UR)-Université de Montpellier (UM)-Avignon Université (AU)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Montpellier 1 (UM1), and Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Adult, Male, Materials science, Physiology, hematocrit, [SDV]Life Sciences [q-bio], Blood viscosity, 030204 cardiovascular system & hematology, Hematocrit, Red blood cell aggregation, Segmental bioelectrical impedance, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, Viscosity, 0302 clinical medicine, Nuclear magnetic resonance, Electrical resistance and conductance, Rheology, Physiology (medical), medicine, Electric Impedance, Humans, Bland–Altman plot, ComputingMilieux_MISCELLANEOUS, Myrenne aggregometer, Leg, medicine.diagnostic_test, Hematology, Venous blood, light transmission, electrical conductance, Blood Viscosity, Hemorheology, Female, Cardiology and Cardiovascular Medicine, Bioelectrical impedance analysis
Abstract: We previously reported that whole body bioelectrical impedance analysis (BIA) measurements are correlated to some hemorheologic factors, suggesting a relationship between viscosity factors and electric properties of flowing blood not only in vitro but also in vivo. Recently we reported that with segmental BIA (analyzing the body considered as composed of 5 cylinders) predictive equations for various determinants of blood viscosity were closer than for the wole body. Another widely used BIA technique uses leg-to-leg impedance measurements so that two cylinders (the two legs) are analyzed. We investigated whether impedance measured with this technique (Tanita TBF-300) is also a predictor of blood viscosity factors. From viscometric measurements performed on venous blood drawn in recreative athletes over the range of shear rates 1 to 6000 s-1 (RHEOMETRE Anton Paar CP 50-1), we found a correlation between leg-leg resistance at 50 kHz (Rx[50 kHz]) and blood viscosity at 1000 s-1 (η1000= 0.0051 Rx[50 kHz] + 1.3265; r = 0.521 p = 0.028 yielding a prediction of η1000 (Bland Altman plot: bias 0.05 [RANGE - 0.24; 0.34]. Neither plasma viscosity nor the red cell rheology index «k» of Quemada's model are correlated with Rx[50 kHz], but hematocrit (Hct) does (Hct (%) = 0.0217 Rx[50 kHz] + 33.783; r = 0.480 p = 0.044) yielding a prediction of Hct (Bland Altman plot: bias - 0.11, [range - 1.67; 1.45]. The discrepancy between actual and predicted Hct is also correlated with resistance at 50 kHz (r = 0.575 p = 0.031) as does the discrepancy between actual and predicted Hct/viscosity ratio (r = -0.651 p = 0.006). Therefore, as other previously studied methods, leg to leg BIA predicts viscosity, suggesting that blood rheology may influence the passage of an electric current in the legs.
Published: 2019
Full Text: View/download PDF

24. Fetal growth retardation and hemorheological predictors of oxygen delivery in hypertensive vs normotensive pregnant women

Author: Céline Roques, Bénédicte Marion, Emmanuelle Varlet-Marie, Eric Raynaud de Mauverger, Jacques Mercier, Pierre Boulot, Jean-Frédéric Brun, Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Adult, medicine.medical_specialty, obesity, Physiology, [SDV]Life Sciences [q-bio], Blood viscosity, Blood Pressure, 030204 cardiovascular system & hematology, Hematocrit, 030218 nuclear medicine & medical imaging, Preeclampsia, preeclampsia, 03 medical and health sciences, small for gestational age, 0302 clinical medicine, Physiology (medical), Internal medicine, medicine, Humans, Blood fluidity, ComputingMilieux_MISCELLANEOUS, Fetal Growth Retardation, medicine.diagnostic_test, business.industry, Infant, Newborn, hypertensive disorders of pregnancy, Gestational age, Hematology, Blood Viscosity, medicine.disease, Oxygen, Low birth weight, medicine.anatomical_structure, Blood pressure, Endocrinology, Hemorheology, Hypertension, Vascular resistance, hemostasis, Small for gestational age, Female, pregnancy, medicine.symptom, Cardiology and Cardiovascular Medicine, business
Abstract: Physiological modifications of blood rheology during pregnancy and their alterations in pregnant hypertensive women have been extensively studied in the 1980's. Since vascular resistance is higher in hypertensive pregnant women whose newborns are small-for gestational-age (SGA), we investigated in a personal database if growth retardation of newborns is related to the oxygen delivery index (ratio hematocrit/blood viscosity) and to the difference between hematocrit (Hct) and the prediction of its optimal valued based on Quemada's equation. A sample of 38 hypertensive pregnant women (age 29 yr±1) was compared with 64 controls matched for age and gestational age, studied at 35±1 weeks gestation, extracted from a larger series of 162 pregnant women. On the whole the hypertensive group gave birth to smaller children (p = 0.014). Plasma viscosity correlated with blood pressure (BP) only in hypertensive women (r = 0.403 p < 0.05). The bell-shaped curve of predicted optimal Hct of non hypertensive pregnant women was similar to that of non-pregnant women, but in hypertensive women it was shifted toward higher values (p = 0.07), and the predicted optimal Hct (but not the actual one) was correlated with systolic blood pressure (SBP) (r = 0.349 p < 0.001) and diastolic blood pressure (DBP) (r = 0.218 p < 0.05). The predicted optimal Hct/viscosity (h/η) ratio was higher in hypertensive women whose newborns exhibited a low birth weight (p = 0.03), resulting in a higher discrepancy between actual and model-predicted «ideal» values of h/η ratio (p = 0.03) and Hct (p = 0.02) compared with the subgroup with no growth retardation. Therefore, in hypertensive women whose newborns exhibited a low birth weight, hemorheological parameters predicting oxygen supply are shifted to lower values than predicted by the model.
Published: 2019
Full Text: View/download PDF

25. Genome sequence of the euryhaline Javafish medaka, Oryzias javanicus: a small aquarium fish model for studies on adaptation to salinity

Author: Amaury Herpin, Manfred Schartl, Shigeki Yasumasu, Cédric Cabau, Koji Inoue, Margot Zahm, Kiyoshi Naruse, Céline Roques, Célia Barrachina, Cécile Donnadieu, Yusuke Takehana, Christophe Klopp, Yann Guiguen, Mari Kawaguchi, Chuya Shinzato, Olivier Bouchez, Laurent Journot, Satoshi Ansai, Nagahama Institute of Bio-Science and Technology, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sophia University, Laboratory of Bioresources, National Institute for Basic Biology [Okazaki], Atmosphere and Ocean Research Institute [Kashiwa-shi] (AORI), The University of Tokyo (UTokyo), Developmental Biochemistry, Biocenter, Julius-Maximilians-Universität Würzburg (JMU), Comprehensive Cancer Center Mainfranken, University Hospital, Hagler Institute for Advanced Study and Department of Biology, Texas A&M University System, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Hunan Normal University (HNU), This work was supported by a 'Projet Incitatif PHASE department 2015' grant (Grant ID ACI_PHASE, Institut National de la Recherche Agronomique) to AH, a NIBB Collaborative Research Initiative to KN, NIBB individual Collaboration Research Project to MK, and Grants-in-Aid for Young Scientists to YT (Grant ID 16K18590) and MK (Grant ID 16K18593). The GeT and MGX core facilities were supported by France Génomique National infrastructure, funded as partof 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). The GeT core facility was also supported by the 409 GET-PACBIO program (« Programme operationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020 »), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-16-COFA-0004,AquaCrispr,Optimization of the CRISPR/Cas9 knock-in technology and application in salmon and trout(2016), ProdInra, Migration, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Optimization of the CRISPR/Cas9 knock-in technology and application in salmon and trout - - AquaCrispr2016 - ANR-16-COFA-0004 - COFA - VALID, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique, Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), The University of Tokyo, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Hunan Normal University, This work was supported by a 'Projet Incitatif PHASE department 2015' grant (Grant ID ACI_PHASE, INRAE) to AH, a NIBB Collaborative Research Initiative to KN, NIBB individual Collaboration Research Project to MK, and Grants-in-Aid for Young Scientists to YT (Grant ID 16K18590) and MK (Grant ID 16K18593). AH was additionally funded by the project AquaCRISPR (ANR-16-COFA-0004-01). The GeT and MGX core facilities were supported by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). The GeT core facility was also supported by the GET-PACBIO program (« Programme opérationnel FEDER-FSE Midi-Pyrénées et Garonne 2014-2020 »), ANR-10- INBS0009,INBS,France-Génomique, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), This work was supported by a 'Projet Incitatif PHASE department 2015' grant (Grant ID ACI_PHASE, INRAE) to AH, a NIBB Collaborative Research Initiative to KN, NIBB individual Collaboration Research Project to MK, and Grants-in-Aid for Young Scientists to YT (Grant ID 16K18590) and MK (Grant ID 16K18593). AH was additionally funded by the project AquaCRISPR (ANR-16-COFA-0004-01). The GeT and MGX core facilities were supported by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). The GeT core facility was also supported by the GET-PACBIO program (« Programme operationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020 »), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1)-Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1), and Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE)
Subjects: 0106 biological sciences, Salinity, carte génétique, Evolution, [SDV]Life Sciences [q-bio], séquençage du génome complet, Sequence assembly, [SDV.GEN] Life Sciences [q-bio]/Genetics, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, QH426-470, Long reads, [INFO] Computer Science [cs], 010603 evolutionary biology, 01 natural sciences, Genome, identification de gènes, adaptation comportementale, 03 medical and health sciences, Genetic map, Genome editing, poisson, Genetics, [INFO]Computer Science [cs], 14. Life underwater, adrianichthyidae, Adaptation, 030304 developmental biology, Whole genome sequencing, tolérance à la salinité, 0303 health sciences, whole genome sequencing, Whole genome sequencing WGS, [SDV.GEN]Life Sciences [q-bio]/Genetics, Phylogenetic tree, biology, Euryhaline, biology.organism_classification, Medaka, osmorégulation, [SDV] Life Sciences [q-bio], [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, espèce modèle, séquençage du génome, eau de mer, Evolutionary biology, Oryzias javanicus, Transcriptome
Abstract: BackgroundThe genus Oryzias is constituted of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behaviour, morphology or adaptation through comparative genomic approaches, all medaka species share many advantages of experimental model organisms including small size and short generation time, transparent embryos and genome editing tools for reverse and forward genetic studies. The Java medaka, Oryzias javanicus, is one of the two species of medaka perfectly adapted for living in brackish/sea-waters. Being an important component of the mangrove ecosystem, O. javanicus is also used as a valuable marine test-fish for ecotoxicology studies. Here, we sequenced and assembled the whole genome of O. javanicus, and anticipate this resource will be catalytic for a wide range of comparative genomic, phylogenetic and functional studies.FindingsComplementary sequencing approaches including long-read technology and data integration with a genetic map allowed the final assembly of 908 Mbp of the O. javanicus genome. Further analyses estimate that the O. javanicus genome contains 33% of repeat sequences and has a heterozygosity of 0.96%. The achieved draft assembly contains 525 scaffolds with a total length of 809.7 Mbp, a N50 of 6.3 Mbp and a L50 of 37 scaffolds. We identified 21454 expressed transcripts for a total transcriptome size of 57, 146, 583 bps.ConclusionsWe provide here a high-quality draft genome assembly of the euryhaline Javafish medaka, and give emphasis on the evolutionary adaptation to salinity.
Published: 2019
Full Text: View/download PDF

26. Development and validation of a liquid chromatography-electrospray ionization-tandem mass spectrometry method for the determination of urolithin C in rat plasma and its application to a pharmacokinetic study

Author: Céline Roques, Gérard Cros, Michel Audran, Françoise M.M. Bressolle-Gomeni, Bénédicte Marion, Morgane Bayle, and Catherine Oiry
Subjects: Male, 0301 basic medicine, Spectrometry, Mass, Electrospray Ionization, Analyte, Formic acid, Clinical Biochemistry, Ethyl acetate, Pharmaceutical Science, Mass spectrometry, Tandem mass spectrometry, 01 natural sciences, Analytical Chemistry, 03 medical and health sciences, chemistry.chemical_compound, Tandem Mass Spectrometry, Drug Discovery, Animals, Rats, Wistar, Spectroscopy, 030109 nutrition & dietetics, Chromatography, 010401 analytical chemistry, Hydrolyzable Tannins, Rats, 0104 chemical sciences, Triple quadrupole mass spectrometer, Urolithin, chemistry, Chromatography, Liquid, Ellagic acid
Abstract: Urolithins are microflora human metabolites of dietary ellagic acid derivatives. There is now a growing interest in the biological activities of these compounds. Several studies suggest that urolithins have potential antioxidant, anti-inflammatory, anticancer and anti-glycative activities. Recently, our group investigated the role of urolithins as potential anti-diabetic treatments; among the four urolithins, urolithin C was the most promising compound. The purpose of this paper was to develop a rapid, sensitive and specific liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) method for the determination of urolithin C in rat plasma. To date, no method is reported for the quantification of urolithin C in any of the matrices. Plasma samples were extracted with ethyl acetate. Urolithin D was selected as the internal standard. The separation was carried out on a C18 Kinetex EVO column (2.1mm×150mm, 2.6μm) using a mobile phase of acetonitrile-1% aqueous formic acid solution (30:70, v/v). A triple quadrupole mass spectrometer in the negative ion mode was used for the determination of the target analyte. The monitored ion transitions were m/z 243→187 for urolithin C and m/z 259→213 for the internal standard. The calibration curve range was 4.95-1085μg/L (r2>0.994). The intra- and inter-day precisions were less than 10%; accuracies ranged from 96.6 to 109%. The mean extraction recovery of urolithins C and D was greater than 91%. No significant matrix effects and no carryover effects were observed. Small changes in LC-ESI-MS/MS conditions did not have significant effect on the determination of urolithin C. Stability tests under various conditions were also investigated. This highly specific and sensitive method was used to analyze samples collected during preclinical pharmacokinetic studies in rats. Glucuronyl and sulfate conjugates of urolithin C were the main metabolites detected in plasma.
Published: 2016
Full Text: View/download PDF

27. Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation

Author: J. Klein, Brianna, Min Jang, Suk, Lachance, Catherine, Mi, Wenyi, Sakuraba, Shun, Krajewski, Krzysztof, Jie Lyu, W. Wang, Wesley, Sidoli, Simone, Yan, Kezhi, Liu, Jiuyang, Zhang, Yi, Céline, Roques, Fournier, Eric, Xiaolu Wang, M. Warfield, Becka, Xiang-Jiao, Yang, A. Garcia, Benjamin, R. Liu, Wenshe, Li, Wei, D. Strahl, Brian, Kono, Hidetoshi, Shi, Xiaobing, Jacques Côté, G. Kutateladze, Tatiana, Shun, Sakuraba, and Hidetoshi, Kono
Abstract: Acetylation of histone H3K23 has emerged as an essential posttranslational modification associated with cancer and learning and memory impairment, yet our understanding of this epigenetic mark remains very limited. Here, we identified the native MORF complex as a histone H3K23-specific acetyltransferase and elucidated its mechanism of action. The acetyltransferase function of the catalytic MORF subunit is positively regulated by the DPF domain of MORF (MORFDPF). The crystal structure of MORFDPF in complex with crotonylated H3K14 peptide provides mechanistic insight into selectivity of this epigenetic reader and its ability to recognize both histone and DNA. Mass spectrometry, biochemical and genomic analyses show co-existence of the H3K23ac and H3K14ac modifications in vitro and co-occupancy of the MORF subunits, H3K23ac, and H3K14ac at promoters of MORF target genes in vivo. Together, our findings reveal a high correlation between two acetylation sites, H3K23 and H3K14, and suggest a model in which interaction of MORFDPF with acylated H3K14 promotes acetylation of H3K23 by the native MORF complex to activate gene transcription.
Published: 2019

28. The RAD51 paralogs ensure cellular protection against mitotic defects and aneuploidy

Author: Amélie Rodrigue, Stéphane Gobeil, Guy G. Poirier, Karine Jacquet, Jean-Yves Masson, Yan Coulombe, Céline Roques, and Jean-Phillipe Gagné
Subjects: DNA, Cruciform, Blotting, Western, Holliday Junction Resolvases, RAD51, Fluorescent Antibody Technique, Mitosis, Cell Biology, Biology, Aneuploidy, Flow Cytometry, Molecular biology, Cell biology, DNA-Binding Proteins, XRCC2, Spindle checkpoint, XRCC3, Holliday junction, Humans, RAD51C, RNA Interference, Homologous recombination, HeLa Cells
Abstract: Summary The interplay between homologous DNA recombination and mitotic progression is poorly understood. The five RAD51 paralogs (RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3) are key enzymes for DNA double-strand break repair. In our search for specific functions of the various RAD51 paralogs, we found that inhibition of XRCC3 elicits checkpoint defects, while inhibition of RAD51B or RAD51C induces G2/M cell cycle arrest in HeLa cells. Using live-cell microscopy we show that in XRCC3-knockdown cells the spindle assembly checkpoint persists and there is a higher frequency of chromosome misalignments, anaphase bridges, and aneuploidy. We observed centrosome defects in the absence of XRCC3. While RAD51B and RAD51C act early in homologous recombination, XRCC3 functions jointly with GEN1 later in the pathway at the stage of Holliday junction resolution. Our data demonstrate that Holliday junction resolution has critical functions for preventing aberrant mitosis and aneuploidy in mitotic cells.
Published: 2013
Full Text: View/download PDF

29. Endoscopic ultrasound-guided fine-needle aspiration plus KRAS and GNAS mutation in malignant intraductal papillary mucinous neoplasm of the pancreas

Author: Pierre Cordelier, Alix Vignolle-Vidoni, Florence Breibach, Nicolas Carrere, Janick Selves, Céline Roques, Jérôme Cros, Fabrice Muscari, Barbara Bournet, Louis Buscail, and David Grand
Subjects: Endoscopic ultrasound, medicine.medical_specialty, Original article, endocrine system diseases, medicine.disease_cause, Malignancy, Gastroenterology, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, medicine, GNAS complex locus, Pharmacology (medical), lcsh:RC799-869, medicine.diagnostic_test, biology, Intraductal papillary mucinous neoplasm, business.industry, medicine.disease, digestive system diseases, 3. Good health, Fine-needle aspiration, medicine.anatomical_structure, Cytopathology, 030220 oncology & carcinogenesis, biology.protein, Cancer research, 030211 gastroenterology & hepatology, lcsh:Diseases of the digestive system. Gastroenterology, KRAS, Pancreas, business
Abstract: Background: KRAS and GNAS mutations are common in intraductal papillary mucinous neoplasia of the pancreas (IPMN). The aims of this study were to assess the role of pre-therapeutic cytopathology combined with KRAS and GNAS mutation assays within cystic fluid sampled by endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) to predict malignancy of IPMN. Patients and methods: We prospectively included 37 IPMN patients with clinical and/or imaging predictors of malignancy (men: 24; mean age: 69.5 years). Cytopathology (performed on cystic fluid and/or IPMN nodules), KRAS (Exon 2, codon 12) and GNAS (Exon 8, codon 201) mutations assays (using TaqMan® allelic discrimination) were performed on EUS-FNA material. The final diagnosis was obtained from IPMN resections (n = 18); surgical biopsies, EUS-FNA analyses, and follow-up (n = 19): 10 and 27 IPMN were benign and malignant, respectively. Results: Sensitivity, specificity, positive and negative predictive values, and accuracy of cytopathology alone to diagnose IPMN malignancy were 55 %, 100 %, 100 %, 45 %, and 66 %, respectively. When KRAS-mutation analysis was combined with cytopathology these values were 92 %, 50 %, 83 %, 71 %, and 81 %, respectively. GNAS assays did not improve the performances of cytopathology alone or those of cytopathology plus a KRAS assay. Conclusions: In patients with a likelihood of malignant IPMN at pre-therapeutic investigation, testing for KRAS mutations in cystic fluid sampling by EUS-FNA improved the results of cytopathology for the diagnosis of malignancy whereas GNAS mutation assay did not.
Published: 2016
Full Text: View/download PDF

30. Recovery of deficient homologous recombination in Brca2-depleted mouse cells by wild-type Rad51 expression

Author: Mark D. Baker, Céline Roques, Shauna A. Lee, Alissa C. Magwood, and Jean-Yves Masson
Subjects: FLP-FRT recombination, Blotting, Western, genetic processes, RAD52, RAD51, Biology, Models, Biological, Biochemistry, Cell Line, Mice, Transformation, Genetic, Animals, RNA, Messenger, Transgenes, skin and connective tissue diseases, Molecular Biology, Cellular localization, Adenosine Triphosphatases, BRCA2 Protein, Recombination, Genetic, Hybridomas, DNA Helicases, Wild type, Nuclear Proteins, Gene targeting, Cell Biology, Molecular biology, Rad52 DNA Repair and Recombination Protein, Non-homologous end joining, Protein Transport, enzymes and coenzymes (carbohydrates), Gene Expression Regulation, Gene Targeting, Mutation, Biocatalysis, health occupations, Rad51 Recombinase, biological phenomena, cell phenomena, and immunity, Homologous recombination, DNA Damage
Abstract: The BRCA2 tumor suppressor is important in maintaining genomic stability. BRCA2 is proposed to control the availability, cellular localization and DNA binding activity of the central homologous recombination protein, RAD51, with loss of BRCA2 resulting in defective homologous recombination. Nevertheless, the roles of BRCA2 in regulating RAD51 and how other proteins implicated in RAD51 regulation, such as RAD52 and RAD54 function relative to BRCA2 is not known. In this study, we tested whether defective homologous recombination in Brca2-depleted mouse hybridoma cells could be rectified by expression of mouse Rad51 or the Rad51-interacting mouse proteins, Rad52 and Rad54. In the Brca2-depleted cells, defective homologous recombination can be restored by over-expression of wild-type mouse Rad51, but not mouse Rad52 or Rad54. Correction of the homologous recombination defect requires Rad51 ATPase activity. A sizeable fraction ( approximately 50%) of over-expressed wild-type Rad51 is nuclear localized. The restoration of homologous recombination in the presence of a low (i.e., non-functional) level of Brca2 by wild-type Rad51 over-expression is unexpected. We suggest that Rad51 may access the nuclear compartment in a Brca2-independent manner and when Rad51 is over-expressed, the normal requirement for Brca2 control over Rad51 function in homologous recombination is dispensable. Our studies support loss of Rad51 function as a critical underlying factor in the homologous recombination defect in the Brca2-depleted cells.
Published: 2009
Full Text: View/download PDF

31. The TIP60 Complex Regulates Bivalent Chromatin Recognition by 53BP1 through Direct H4K20me Binding and H2AK15 Acetylation

Author: Gaëlle Legube, Jean-Philippe Lambert, Yannick Doyon, Karine Jacquet, Pauline M. Herst, Anne-Claude Gingras, Eric Paquet, Raj K. Pandita, Amélie Fradet-Turcotte, Daniel Durocher, Jacques Côté, Nikita Avvakumov, Céline Roques, and Tej K. Pandita
Subjects: 0301 basic medicine, Time Factors, DNA Repair, Transcription, Genetic, Chromosomal Proteins, Non-Histone, Biology, Transfection, Binding, Competitive, Chromatin remodeling, Lysine Acetyltransferase 5, Article, Histones, 03 medical and health sciences, Histone methylation, Humans, Acetyltransferase complex, DNA Breaks, Double-Stranded, Promoter Regions, Genetic, Molecular Biology, Histone Acetyltransferases, Binding Sites, Ubiquitination, Acetylation, Cell Biology, Chromatin Assembly and Disassembly, Molecular biology, Chromatin, Cell biology, Repressor Proteins, 030104 developmental biology, Histone, biology.protein, RNA Interference, CRISPR-Cas Systems, K562 Cells, Tumor Suppressor p53-Binding Protein 1, Protein Processing, Post-Translational, Bivalent chromatin, Protein Binding, Signal Transduction
Abstract: The NuA4/TIP60 acetyltransferase complex is a key regulator of genome expression and stability. Here, we identified MBTD1 as a new stable subunit of the complex and gleaned intriguing insights into TIP60’s function. Harboring a histone reader domain for H4K20me1/2, MBTD1 allows TIP60 to associate with specific gene promoters and to promote the repair of DNA double strand breaks by homologous recombination. Interestingly, the non-homologous end joining factor 53BP1 engages chromatin through simultaneous binding of H4K20me2 and H2AK15ub, and it was postulated that Tip60-dependent acetylation of H4 regulates this binding. Our findings now indicate that the TIP60 complex is a potent regulator of DNA damage repair pathways in part by targeting the same histone mark as 53BP1. In addition, deposition of H2AK15ub by RNF168 inhibits chromatin acetylation by TIP60, while this residue can be acetylated by TIP60 in vivo, blocking its ubiquitylation. Altogether, these results uncover an intricate mechanism orchestrated by the TIP60 complex which regulates 53BP1-dependent repair pathway selection through incompatible bivalent binding and modification of chromatin.
Published: 2015

32. A Scalable Genome-Editing-Based Approach for Mapping Multiprotein Complexes in Human Cells

Author: Karine Jacquet, Caroline C. Huard, Jacques Côté, Céline Roques, Jeremy Loehr, Pauline M. Herst, Mathieu Dalvai, and Yannick Doyon
Subjects: Genetics, Proteomics, Transcription activator-like effector nuclease, Minichromosome Maintenance Proteins, Cas9, Genome, Human, Computational biology, Biology, Genome, General Biochemistry, Genetics and Molecular Biology, Protein–protein interaction, lcsh:Biology (General), Genome editing, TAL effector, Cell Line, Tumor, Gene Targeting, CRISPR, Humans, CRISPR-Cas Systems, lcsh:QH301-705.5, Protein Binding
Abstract: SummaryConventional affinity purification followed by mass spectrometry (AP-MS) analysis is a broadly applicable method used to decipher molecular interaction networks and infer protein function. However, it is sensitive to perturbations induced by ectopically overexpressed target proteins and does not reflect multilevel physiological regulation in response to diverse stimuli. Here, we developed an interface between genome editing and proteomics to isolate native protein complexes produced from their natural genomic contexts. We used CRISPR/Cas9 and TAL effector nucleases (TALENs) to tag endogenous genes and purified several DNA repair and chromatin-modifying holoenzymes to near homogeneity. We uncovered subunits and interactions among well-characterized complexes and report the isolation of MCM8/9, highlighting the efficiency and robustness of the approach. These methods improve and simplify both small- and large-scale explorations of protein interactions as well as the study of biochemical activities and structure-function relationships.
Published: 2015

33. BRPF3-HBO1 regulates replication origin activation and histone H3K14 acetylation

Author: Yunpeng Feng, Arsenios Vlassis, Xiang-Jiao Yang, Cristina González-Aguilera, Sung Bau Lee, Anne-Claude Gingras, Eric Paquet, Xiaobei Zhao, Jacques Côté, Céline Roques, Anja Groth, Jens Vilstrup Johansen, Jean-Philippe Lambert, Marie-Eve Lalonde, and Constance Alabert
Subjects: 0301 basic medicine, DNA Replication, Chromatin Immunoprecipitation, Eukaryotic DNA replication, Replication Origin, Pre-replication complex, General Biochemistry, Genetics and Molecular Biology, Cell Line, DNA replication factor CDT1, Histones, 03 medical and health sciences, Replication factor C, Minichromosome maintenance, Control of chromosome duplication, Humans, Molecular Biology, Histone Acetyltransferases, Genetics, General Immunology and Microbiology, biology, General Neuroscience, Cell Cycle, Acetylation, Articles, Immunohistochemistry, Chromatin, Cell biology, 030104 developmental biology, Licensing factor, biology.protein, Origin recognition complex
Abstract: During DNA replication, thousands of replication origins are activated across the genome. Chromatin architecture contributes to origin specification and usage, yet it remains unclear which chromatin features impact on DNA replication. Here, we perform a RNAi screen for chromatin regulators implicated in replication control by measuring RPA accumulation upon replication stress. We identify six factors required for normal rates of DNA replication and characterize a function of the bromodomain and PHD finger-containing protein 3 (BRPF3) in replication initiation. BRPF3 forms a complex with HBO1 that specifically acetylates histone H3K14, and genomewide analysis shows high enrichment of BRPF3, HBO1 and H3K14ac at ORC1-binding sites and replication origins found in the vicinity of TSSs. Consistent with this, BRPF3 is necessary for H3K14ac at selected origins and efficient origin activation. CDC45 recruitment, but not MCM2-7 loading, is impaired in BRPF3-depleted cells, identifying a BRPF3-dependent function of HBO1 in origin activation that is complementary to its role in licencing. We thus propose that BRPF3-HBO1 acetylation of histone H3K14 around TSS facilitates efficient activation of nearby replication origins.
Published: 2015

34. MRE11–RAD50–NBS1 is a critical regulator of FANCD2 stability and function during DNA double-strand break repair

Author: Amélie Rodrigue, Jean-Yves Masson, Mathieu Delannoy, Isabelle Brodeur, Simona Grossi, Jean Gautier, Angelos Constantinou, Céline Roques, Andrzej Stasiak, Alicja Z. Stasiak, Julien Vignard, Yan Coulombe, Laval University Cancer Research Center - Genome Stability Laboratory, Université Laval [Québec] (ULaval), BIL Biomedical Research Center, Columbia University [New York], Faculty of Biology and Medicine, Center for Integrative Genomics, Université de Lausanne, and Hôpital Hôtel-Dieu
Subjects: congenital, hereditary, and neonatal diseases and abnormalities, DNA Repair, DNA damage, DNA repair, [SDV]Life Sciences [q-bio], Down-Regulation, Cell Cycle Proteins, homologous recombination, fanconi anaemia, Biology, mirin, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, DNA metabolism, MRE11 Homologue Protein, hemic and lymphatic diseases, Humans, DNA Breaks, Double-Stranded, RNA, Small Interfering, Molecular Biology, Replication protein A, 030304 developmental biology, 0303 health sciences, General Immunology and Microbiology, Protein Stability, General Neuroscience, Fanconi Anemia Complementation Group D2 Protein, Nuclear Proteins, nutritional and metabolic diseases, Molecular biology, Double Strand Break Repair, Acid Anhydride Hydrolases, DNA-Binding Proteins, Microscopy, Electron, enzymes and coenzymes (carbohydrates), DNA Repair Enzymes, chemistry, 030220 oncology & carcinogenesis, Rad50, Biophysics, Homologous recombination, DNA, HeLa Cells, Protein Binding
Abstract: International audience; Monoubiquitination of the Fanconi anaemia protein FANCD2 is a key event leading to repair of interstrand cross-links. It was reported earlier that FANCD2 co-localizes with NBS1. However, the functional connection between FANCD2 and MRE11 is poorly understood. In this study, we show that inhibition of MRE11, NBS1 or RAD50 leads to a destabilization of FANCD2. FANCD2 accumulated from mid-S to G2 phase within sites containing single-stranded DNA (ssDNA) intermediates, or at sites of DNA damage, such as those created by restriction endonucleases and laser irradiation. Purified FANCD2, a ring-like particle by electron microscopy, preferentially bound ssDNA over various DNA substrates. Inhibition of MRE11 nuclease activity by Mirin decreased the number of FANCD2 foci formed in vivo. We propose that FANCD2 binds to ssDNA arising from MRE11-processed DNA double-strand breaks. Our data establish MRN as a crucial regulator of FANCD2 stability and function in the DNA damage response.
Published: 2009
Full Text: View/download PDF

35. FANCD2: A DNA binding protein regulated by MRE11-RAD50-NBS1

Author: Céline Roques and Jean-Yves Masson
Subjects: HMG-box, Cell Cycle Proteins, Pyrimidinones, Single-stranded binding protein, Mice, DDB1, Animals, DNA Breaks, Double-Stranded, RNA, Small Interfering, Molecular Biology, Replication protein A, MRE11 Homologue Protein, biology, Fanconi Anemia Complementation Group D2 Protein, Binding protein, Nuclear Proteins, Thiones, Cell Biology, DNA-binding domain, Acid Anhydride Hydrolases, Cell biology, DNA-Binding Proteins, DNA binding site, DNA Repair Enzymes, biology.protein, ATP-Binding Cassette Transporters, Developmental Biology, Binding domain
Published: 2010
Full Text: View/download PDF

36. The rise and fall of the ancient northern pike master sex-determining gene

Author: Qiaowei Pan, Romain Feron, Elodie Jouanno, Hugo Darras, Amaury Herpin, Ben Koop, Eric Rondeau, Frederick W Goetz, Wesley A Larson, Louis Bernatchez, Mike Tringali, Stephen S Curran, Eric Saillant, Gael PJ Denys, Frank A von Hippel, Songlin Chen, J Andrés López, Hugo Verreycken, Konrad Ocalewicz, Rene Guyomard, Camille Eche, Jerome Lluch, Celine Roques, Hongxia Hu, Roger Tabor, Patrick DeHaan, Krista M Nichols, Laurent Journot, Hugues Parrinello, Christophe Klopp, Elena A Interesova, Vladimir Trifonov, Manfred Schartl, John Postlethwait, and Yann Guiguen
Subjects: fish, pikes, mudminnows, esociforms, esocidae, umbridae, Medicine, Science, Biology (General), QH301-705.5
Abstract: The understanding of the evolution of variable sex determination mechanisms across taxa requires comparative studies among closely related species. Following the fate of a known master sex-determining gene, we traced the evolution of sex determination in an entire teleost order (Esociformes). We discovered that the northern pike (Esox lucius) master sex-determining gene originated from a 65 to 90 million-year-old gene duplication event and that it remained sex linked on undifferentiated sex chromosomes for at least 56 million years in multiple species. We identified several independent species- or population-specific sex determination transitions, including a recent loss of a Y chromosome. These findings highlight the diversity of evolutionary fates of master sex-determining genes and the importance of population demographic history in sex determination studies. We hypothesize that occasional sex reversals and genetic bottlenecks provide a non-adaptive explanation for sex determination transitions.
Published: 2021
Full Text: View/download PDF

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Publication Type

Journal

Database

Publisher

36 results on '"Céline Roques"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources